Molecular Dynamics applications enhance our understanding of
biological phenomena through bio-molecular simulations. Large-scale
parallelization of MD simulations is challenging because of the
small number of atoms and small time scales involved. Load
balancing in parallel MD programs is crucial for good performance
on large parallel machines. This paper discusses load balancing
algorithms deployed in a MD code called NAMD. It focuses on new
schemes deployed in the load balancers and provides an analysis of
the performance benefits achieved. Specifically, the paper presents
the technique of topology-aware mapping on 3D mesh and torus
architectures, used to improve scalability and performance. These
techniques have a wide applicability for latency intolerant
applications.